Linked Life Data

20568719

Source:http://linkedlifedata.com/resource/pubmed/id/20568719

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
14
pubmed:dateCreated
2010-7-29
pubmed:abstractText
Data dependent neutral loss triggered MS3 methodology (NLMS3) is often applied to acquire MS data for the analysis of phosphopeptides. Some phosphopeptides tend to seriously lose the phosphate and result in MS2 spectra with poor fragments and fragment-rich MS3 spectra, while some phosphopeptides do not lose phosphate and result in nice MS2 spectra. Since different phosphopeptides have fragment spectra with different characteristics, filtering all of the phosphopeptide identifications by setting a global filter criteria may be inappropriate and result in low sensitivity. In this study, we developed a classification filtering strategy to improve the phosphopeptide identification and phosphorylation site localization. Phosphopeptide identifications were classified into four classes according to their different characteristics, and then, the identifications from each class of mass spectra were processed and filtered separately using different filtering strategies. It was found that the overlap of phosphopeptide identifications from different classes was low and the classification strategy significantly improved the coverage of the phosphoproteome analysis. Compared with MS2 strategy and multiple stage activation (MSA) strategy, NLMS3 with the classification filtering strategy was demonstrated to have higher sensitivity and higher performance in localizing the phosphorylation to specific sites.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
1520-6882
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
82
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
6168-75
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
Classification filtering strategy to improve the coverage and sensitivity of phosphoproteome analysis.
pubmed:affiliation
CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't